When does CodeIgniter return 404 headers, exactly?

[eluser]besson3c[/eluser]
For some reason, the URLs associated with my CodeIgniter app are returning 404 errors according to my browser's logs. The content associated with these pages returns fine, there is no noticeable problem that can be seen through the browser with one exception...

The exception is with Prototype apps that utilize the "onSuccess" callback. Because these URLs are all generating 404 headers, this callback is not triggered - I have to use the onComplete callback instead.

Again, to re-emphasize, I'm not getting the 404 error message page, my pages are rendering their correct content as expected. There is clearly something related to the way my content is served by the server that is triggering these headers, and I'm trying to trace down what the cause might be?

My .htaccess file is pretty standard:

RewriteCond $1 !^(index\.php|albumimages|wordpress|styles|js|nm_webkit|robots\.txt)
RewriteRule ^(.*)$ /index.php/main/$1 [L]

I still get 404 errors appearing in my log files when I access my controller's functions via:

http://mydomain/index.php/mycontroller/myfunction

So, I'm not convinced that the problem is with mod_rewrite. I'm not seeing any 404 messages in my CodeIgniter logs, it appears to be happily serving these pages with the final log message "Final output sent to browser" and its total execution time (I'm also getting this output in my browser, like I said).

Any other ideas as to what might be causing these 404 headers being sent?